Ncbi Gene Tools#

Configuration File: ncbi_gene_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the ncbi_gene_tools.json configuration file.

Available Tools#

NCBIGene_get_summary (Type: BaseRESTTool)#

Get a detailed gene summary from NCBI Gene by Entrez Gene ID using the E-utilities ESummary API. …

NCBIGene_get_summary tool specification

Tool Information:

  • Name: NCBIGene_get_summary

  • Type: BaseRESTTool

  • Description: Get a detailed gene summary from NCBI Gene by Entrez Gene ID using the E-utilities ESummary API. Returns gene name, symbol, description, function summary, chromosomal location, map position, aliases, genomic coordinates, exon count, and MIM (OMIM) IDs. The most authoritative source for human gene information. Use NCBIGene_search first to find Gene IDs. Example: Gene ID 7157 returns TP53 on chromosome 17p13.1 with a detailed functional summary.

Parameters:

  • id (string) (required) NCBI Gene ID (Entrez Gene ID). Can be a single ID or comma-separated list. Examples: ‘7157’ (TP53), ‘672’ (BRCA1), ‘1956’ (EGFR), ‘3845’ (KRAS). Get IDs from NCBIGene_search.

Example Usage:

query = {
    "name": "NCBIGene_get_summary",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)

NCBIGene_search (Type: BaseRESTTool)#

Search NCBI Gene using ESearch with explicit offset pagination and normalized exact metadata. Con…

NCBIGene_search tool specification

Tool Information:

  • Name: NCBIGene_search

  • Type: BaseRESTTool

  • Description: Search NCBI Gene using ESearch with explicit offset pagination and normalized exact metadata. Continue with metadata.next_retstart while metadata.has_more is true. Raw ESearch count/retstart/retmax values remain available as strings in data.esearchresult; metadata exposes their validated integer form.

Parameters:

  • term (string) (required) Search query. Use gene symbol with organism filter for best results. Format: ‘GENE[Symbol] AND Organism[Organism]’. Examples: ‘TP53[Symbol] AND Homo sapiens[Organism]’, ‘BRCA1[Symbol] AND Homo sapiens[Organism]’, ‘insulin AND Homo sapiens[Organism]’, ‘EGFR AND Mus musculus[Organism]’.

  • retmax (integer) (optional) Page size (1-100).

  • retstart (integer) (optional) Zero-based result offset. Use esearchresult.retstart plus the number of returned IDs to retrieve the next page while it remains below esearchresult.count.

Example Usage:

query = {
    "name": "NCBIGene_search",
    "arguments": {
        "term": "example_value"
    }
}
result = tu.run(query)

NCBIProtein_get_summary (Type: BaseRESTTool)#

Get protein record summary from the NCBI Protein database by GI number or accession using the E-u…

NCBIProtein_get_summary tool specification

Tool Information:

  • Name: NCBIProtein_get_summary

  • Type: BaseRESTTool

  • Description: Get protein record summary from the NCBI Protein database by GI number or accession using the E-utilities ESummary API. Returns protein title, organism, accession version, sequence length, molecular type, source database, and creation/update dates. NCBI Protein aggregates sequences from GenBank, RefSeq, Swiss-Prot, PDB, and other sources. Use for resolving NCBI protein GI numbers to names, accessions, and species. Example: GI 119395750 returns ‘keratin, type II cytoskeletal 1 [Homo sapiens]’ with accession NP_006112.3 and length 644 aa.

Parameters:

  • id (string) (required) NCBI Protein ID (GI number or accession). Can be a single ID or comma-separated list. Examples: ‘119395750’ (keratin 1, NP_006112), ‘4507879’ (TP53, NP_000537), ‘4503747’ (EGFR, NP_005219). GI numbers can be obtained from NCBI Gene genomic info or from BLAST results.

Example Usage:

query = {
    "name": "NCBIProtein_get_summary",
    "arguments": {
        "id": "example_value"
    }
}
result = tu.run(query)